Genome-wide investigation reveals high evolutionary rates in annual model plants

Background: ;Rates of molecular evolution vary widely among species. While significant deviations from molecular clock have been found in many taxa, effects of life histories on molecular evolution are not fully understood. In plants, annual/perennial life history traits have long been suspected to influence the evolutionary rates at the molecular level. To date, however, the number of genes investigated on this subject is limited and the conclusions are mixed. To evaluate the possible heterogeneity in evolutionary rates between annual and perennial plants at the genomic level, we investigated 85 nuclear housekeeping genes, 10 non-housekeeping families, and 34 chloroplast;genes using the genomic data from model plants including Arabidopsis thaliana and Medicago truncatula for annuals and grape (Vitis vinifera) and popular (Populus trichocarpa) for perennials.;Results: ;According to the cross-comparisons among the four species, 74-82% of the nuclear genes and 71-97% of the chloroplast genes suggested higher rates of molecular evolution in the two annuals than those in the two perennials. The significant heterogeneity in evolutionary rate between annuals and perennials was consistently found both in nonsynonymous sites and synonymous sites. While a linear correlation of evolutionary rates in orthologous genes between species was observed in nonsynonymous sites, the correlation was weak or invisible in synonymous sites. This tendency was clearer in nuclear genes than in chloroplast genes, in which the overall;evolutionary rate was small. The slope of the regression line was consistently lower than unity, further confirming the higher evolutionary rate in annuals at the genomic level.;Conclusions: ;The higher evolutionary rate in annuals than in perennials appears to be a universal phenomenon both in nuclear and chloroplast genomes in the four dicot model plants we investigated. Therefore, such heterogeneity in evolutionary rate should result from factors that have genome-wide influence, most likely those associated with annual/perennial life history. Although we acknowledge current limitations of this kind of study, mainly due to a small sample size available and a distant taxonomic relationship of the model organisms, our results indicate that the genome-wide survey is a promising approach toward further understanding of the;mechanism determining the molecular evolutionary rate at the genomic level.

High colonization rates of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli in Swiss Travellers to South Asia- a prospective observational multicentre cohort study looking at epidemiology, microbiology and risk factors.

BACKGROUND International travel contributes to the worldwide spread of multidrug resistant Gram-negative bacteria. Rates of travel-related faecal colonization with extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae vary for different destinations. Especially travellers returning from the Indian subcontinent show high colonization rates. So far, nothing is known about region-specific risk factors for becoming colonized. METHODS An observational prospective multicentre cohort study investigated travellers to South Asia. Before and after travelling, rectal swabs were screened for third-generation cephalosporin- and carbapenem-resistant Enterobacteriaceae. Participants completed questionnaires to identify risk factors for becoming colonized. Covariates were assessed univariately, followed by a multivariate regression. RESULTS Hundred and seventy persons were enrolled, the largest data set on travellers to the Indian subcontinent so far. The acquired colonization rate with ESBL-producing Escherichia coli overall was 69.4% (95% CI 62.1-75.9%), being highest in travellers returning from India (86.8%; 95% CI 78.5-95.0%) and lowest in travellers returning from Sri Lanka (34.7%; 95% CI 22.9-48.7%). Associated risk factors were travel destination, length of stay, visiting friends and relatives, and eating ice cream and pastry. CONCLUSIONS High colonization rates with ESBL-producing Enterobacteriaceae were found in travellers returning from South Asia. Though risk factors were identified, a more common source, i.e. environmental, appears to better explain the high colonization rates.

Draft Genome Sequence of the Virulent Clostridium chauvoei Reference Strain JF4335

Clostridium chauvoei is the etiological agent of blackleg, a disease of cattle and sheep with high mortality rates, causing severe economic losses in livestock production. Here, we report the draft genome sequence of the virulent C. chauvoei strain JF4335 (2.8 Mbp and 28% G+C content) and the annotation of the genome.

Complication and failure rates of fixed dental prostheses in patients treated for periodontal disease

Objectives: To evaluate the biological and technical complication rates of fixed dental prostheses (FDP) with end abutments or cantilever extensions on teeth (FDP-tt/cFDP-tt) on implants (FDP-ii/cFDP-ii) and tooth-implant-supported (FDP-ti/cFDP-ti) in patients treated for chronic periodontitis. Material and methods: From a cohort of 392 patients treated between 1978 and 2002 by graduate students, 199 were re-examined in 2005. Of these, 84 patients had received ceramo-metal FDPs (six groups). Results: At the re-evaluation, the mean age of the patients was 62 years (36.2–83.4). One hundred and seventy-five FDPs were seated (82 FDP-tt, 9 FDP-ii, 20 FDP-ti, 39 cFDP-tt, 15 cFDP-ii, 10 cFDP-ti). The mean observation time was 11.3 years; 21 FDPs were lost, and 46 technical and 50 biological complications occurred. Chances for the survival of the three groups of FDPs with end abutments were very high (risk for failure 2.8%, 0%, 5.6%). The probability to remain without complications and/or failure was 70.3%, 88.9% and 74.7% in FDPs with end abutments, but 49.8–25% only in FDPs with extensions at 10 years. Conclusions: In patients treated for chronic periodontitis and provided with ceramo-metal FDPs, high survival rates, especially for FDPs with end abutments, can be expected. The incidence rates of any negative events were increased drastically in the three groups with extension cFDPs (tt, ii, ti). Strategic decisions in the choice of a particular FDP design and the choice of teeth/implants as abutments appear to influence the risks for complications to be expected with fixed reconstruction. If possible, extensions on tooth abutments should be avoided or used only after a cautious clinical evaluation of all options.

A Method for Detecting Population Genetic Structure in Diverse, High Gene-Flow Species

Detecting small amounts of genetic subdivision across geographic space remains a persistent challenge. Often a failure to detect genetic structure is mistaken for evidence of panmixia, when more powerful statistical tests may uncover evidence for subtle geographic differentiation. Such slight subdivision can be demographically and evolutionarily important as well as being critical for management decisions. We introduce here a method, called spatial analysis of shared alleles (SAShA), that detects geographically restricted alleles by comparing the spatial arrangement of allelic co-occurrences with the expectation under panmixia. The approach is allele-based and spatially explicit, eliminating the loss of statistical power that can occur with user-defined populations and statistical averaging within populations. Using simulated data sets generated under a stepping-stone model of gene flow, we show that this method outperforms spatial autocorrelation (SA) and UST under common real-world conditions: at relatively high migration rates when diversity is moderate or high, especially when sampling is poor. We then use this method to show clear differences in the genetic patterns of 2 nearshore Pacific mollusks, Tegula funebralis (5 Chlorostoma funebralis) and Katharina tunicata, whose overall patterns of within-species differentiation are similar according to traditional population genetics analyses. SAShA meaningfully complements UST/FST, SA, and other existing geographic genetic analyses and is especially appropriate for evaluating species with high gene flow and subtle genetic differentiation.

A systematic review of the 5-year survival and complication rates of implant-supported single crowns

OBJECTIVES: The objective of this systematic review was to assess the 5-year survival of implant-supported single crowns (SCs) and to describe the incidence of biological and technical complications. METHODS: An electronic MEDLINE search complemented by manual searching was conducted to identify prospective and retrospective cohort studies on SCs with a mean follow-up time of at least 5 years. Failure and complication rates were analyzed using random-effects Poisson's regression models to obtain summary estimates of 5-year proportions. RESULTS: Twenty-six studies from an initial yield of 3601 titles were finally selected and data were extracted. In a meta-analysis of these studies, survival of implants supporting SCs was 96.8% [95% confidence interval (CI): 95.9-97.6%] after 5 years. The survival rate of SCs supported by implants was 94.5% (95% CI: 92.5-95.9%) after 5 years of function. The survival rate of metal-ceramic crowns, 95.4% (95% CI: 93.6-96.7%), was significantly (P=0.005) higher than the survival rate, 91.2% (95% CI: 86.8-94.2%), of all-ceramic crowns. Peri-implantitis and soft tissue complications occurred adjacent to 9.7% of the SCs and 6.3% of the implants had bone loss exceeding 2 mm over the 5-year observation period. The cumulative incidence of implant fractures after 5 years was 0.14%. After 5 years, the cumulative incidence of screw or abutment loosening was 12.7% and 0.35% for screw or abutment fracture. For supra-structure-related complications, the cumulative incidence of ceramic or veneer fractures was 4.5%. CONCLUSION: It can be concluded that after an observation period of 5 years, high survival rates for implants and implant-supported SCs can be expected. However, biological and particularly technical complications are frequent.

From transient to steady state deformation and grain size: A thermodynamic approach using elasto-visco-plastic numerical modeling

Numerical simulation experiments give insight into the evolving energy partitioning during high-strain torsion experiments of calcite. Our numerical experiments are designed to derive a generic macroscopic grain size sensitive flow law capable of describing the full evolution from the transient regime to steady state. The transient regime is crucial for understanding the importance of micro structural processes that may lead to strain localization phenomena in deforming materials. This is particularly important in geological and geodynamic applications where the phenomenon of strain localization happens outside the time frame that can be observed under controlled laboratory conditions. Ourmethod is based on an extension of the paleowattmeter approach to the transient regime. We add an empirical hardening law using the Ramberg-Osgood approximation and assess the experiments by an evolution test function of stored over dissipated energy (lambda factor). Parameter studies of, strain hardening, dislocation creep parameter, strain rates, temperature, and lambda factor as well asmesh sensitivity are presented to explore the sensitivity of the newly derived transient/steady state flow law. Our analysis can be seen as one of the first steps in a hybrid computational-laboratory-field modeling workflow. The analysis could be improved through independent verifications by thermographic analysis in physical laboratory experiments to independently assess lambda factor evolution under laboratory conditions.

Analysis of caesarean section rates over time in a single Swiss centre using a ten-group classification system.

OBJECTIVE Caesarean section (CS) rates have risen over the past two decades. The aim of this observational study was to identify time-dependent variations in CS and vaginal delivery rates over a period of 11 years. METHOD All deliveries (13,701 deliveries during the period 1999-2009) at the University Women's Hospital Bern were analysed using an internationally standardised and approved ten-group classification system. Caesarean sections on maternal request (CSMR) were evaluated separately. RESULTS We detected an overall CS rate of 36.63% and an increase in the CS rate over time (p <0.001). Low-risk profile groups were the two largest populations and displayed low CS rates, with significantly decreasing relative size over time. The relative size of groups with induced labour increased significantly, but this did not have an impact on the overall CS rate. Pregnancies complicated by breech position, multiple pregnancies and abnormal lies did not have an impact on overall CS rate. The biggest contributor to a high CS rate was preterm delivery and the existence of a uterine scar from a previous CS. CSMR was 1.45% and did not have an impact on the overall CS rate. CONCLUSION The observational study identified wide variations in caesarean section and vaginal delivery rates across the groups over time, and a shift towards high-risk populations was noted. The biggest contributors to high CS rates were identified; namely, previous uterine scar and preterm delivery. Interventions aiming to reduce CS rates are planned.

Microfabric memory of vein quartz for strain localization in detachment faults: A case study on the Simplon fault zone

This manuscript deals with the adaptation of quartz-microfabrics to changing physical deformation conditions, and discusses their preservation potential during subsequent retrograde deformation. Using microstructural analysis, a sequence of recrystallization processes in quartz, ranging from Grain-Boundary Migration Recrystallization (GBM) over Subgrain-Rotation Recrystallization (SGR) to Bulging Nucleation (BLG) is detected for the Simplon fault zone (SFZ) from the low strain rim towards the internal high strain part of the large-scale shear zone. Based on: (i) the retrograde cooling path; (ii) estimates of deformation temperatures; and (iii) spatial variation of dynamic recrystallization processes and different microstructural characteristics, continuous strain localization with decreasing temperature is inferred. In contrast to the recrystallization microstructures, crystallographic preferred orientations (CPO) have a longer memory. CPO patterns indicative of prism and rhomb glide systems in mylonitic quartz veins, overprinted at low temperatures (�400 �C), suggest inheritance of a high-temperature deformation. In this way, microstructural, textural and geochemical analyses provide information for several million years of the deformation history. The reasons for such incomplete resetting of the rock texture is that strain localization is caused by change in effective viscosity contrasts related to temporal large- and small-scale temperature changes during the evolution of such a long-lived shear zone. The spatially resolved, quantitative investigation of quartz microfabrics and associated recrystallization processes therefore provide great potential for an improved understanding of the geodynamics of large-scale shear zones.

Complication and failure rates with implant-supported fixed dental prostheses and single crowns: a 10-year retrospective study

PURPOSE Clinical studies related to the long-term outcomes with implant-supported reconstructions are still sparse. The aim of this 10-year retrospective study was to assess the rate of mechanical/technical complications and failures with implant supported fixed dental prostheses (FDPs) and single crowns (SCs) in a large cohort of partially edentulous patients. MATERIALS AND METHODS The comprehensive multidisciplinary examination consisted of a medical/dental history, clinical examination, and a radiographic analysis. Prosthodontic examination evaluated the implant-supported reconstructions for mechanical/technical complications and failures, occlusal analysis, presence/absence of attrition, and location, extension, and retention type. RESULTS Out of three hundred ninety seven fixed reconstructions in three hundred three patients, two hundred sixty eight were SCs and one hundred twenty seven were FDPs. Of these three hundred ninety seven implant-supported reconstructions, 18 had failed, yielding a failure rate of 4.5% and a survival rate of 95.5% after a mean observation period of 10.75 years (range: 8.4-13.5 years). The most frequent complication was ceramic chipping (20.31%) followed by occlusal screw loosening (2.57%) and loss of retention (2.06%). No occlusal screw fracture, one abutment loosening, and two abutment fractures were noted. This resulted in a total mechanical/technical complication rate of 24.7%. The prosthetic success rate over a mean follow-up time of 10.75 years was 70.8%. Generalized attrition and FDPs were associated with statistically significantly higher rates of ceramic fractures when compared with SCs. Cantilever extensions, screw retention, anterior versus posterior, and gender did not influence the chipping rate. CONCLUSIONS After a mean exposure time of 10.75 years, high survival rates for reconstructions supported by Sand-blasted Large-grit Acid-etched implants can be expected. Ceramic chipping was the most frequent complication and was increased in dentitions with attrition and in FDPs compared with SCs.

Small quantity but large effect — How minor phases control strain localization in upper mantle shear zones

Low viscosity domains such as localized shear zones exert an important control on the geodynamics of the uppermost mantle. Grain size reduction and subsequent strain localization related to a switch from dislocation to diffusion creep is one mechanism to form low viscosity domains. To sustain strain localization, the grain size of mantle minerals needs to be kept small over geological timescales. One way to keep olivine grain sizes small is by pinning of mobile grain boundaries during grain growth by other minerals (second phases). Detailed microstructural studies based on natural samples from three shear zones formed at different geodynamic settings, allowed the derivation of the olivine grain-size dependence on the second-phase content. The polymineralic olivine grain-size evolution with increasing strain is similar in the three shear zones. If the second phases are to pin the mobile olivine grain boundary the phases need to be well mixed before grain growth. We suggest that melt-rock and metamorphic reactions are crucial for the initial phase mixing in mantle rocks. With ongoing deformation and increasing strain, grain boundary sliding combined with mass transfer processes and nucleation of grains promotes phase mixing resulting in fine-grained polymineralic mixtures that deform by diffusion creep. Strain localization due to the presence of volumetrically minor minerals in polymineralic mantle rocks is only important at high strain deformation (ultramylonites) at low temperatures (<~800°C). At smaller strain and stress conditions and/or higher temperatures other parameters like overall energy available to deform a given rock volume, the inheritance of mechanical anisotropies or the presence of water or melts needs to be considered to explain strain localization in the upper mantle.

Explosive speciation rates and unusual species richness in haplochromine cichlid fishes: Effects of sexual selection

Ancient lakes are often unusually species rich, mostly as a result of radiation and species-flock formation having taken place in only one or a few of many taxa present. Understanding why some taxa radiate and others do not is at the heart of understanding biodiversity. In this chapter I discuss possible explanations for disproportionally large species numbers in some cichlid fish lineages in East African Great Lakes: the halochromine cichlid fishes in Lakes Victoria and Malawi. I show that speciation rates in this group are higher than in any other lacustrine fish radiation. Against this background, I review hypotheses put forward to explain diversity in cichlid species flocks. The evolution of species diversity requires three processes: speciation, ecological radiation and anatomical diversification, and it is wrong to consider hypotheses that are relevant to different processes as alternatives to each other. The African cichlid species flocks show unusually high ecological species packing in several phylogenetic groups and unusually high speciation rates in haplochromines. Therefore, it maybe concluded that at least two evolutionary models are required to explain the difference between cichlid diversity and other fish diversity in East African Lakes: one for speciation in haplochromines and one for coexistence. Subsequently I review work on speciation in haplochromines, and in particular studies aimed at testing the hypothesis of speciation by sexual selection. Haplochromines have a polygynous mating system, conducive to sexual selection, but other polygynous cichlids are not particularly species rich. This suggests that more than just strong sexual selection is required to explain haplochromine species richness. Recent palaeoecological evidence undermines the previously popular hypotheses that explained the species richness of Lake Victoria in terms of speciation under varying natural or sexual selection regimes in satellite lakes or in isolated lake basins. I summarize experimental and comparative studies, which provide evidence for two mechanisms of sympatric speciation by disruptive sexual selection on polymorphic coloration. Such modes of speciation may explain (i) the high speciation rates in colour polymorphic lineages of haplochromine cichlids under conditions where colour variation is visible in clear water, and (ii) in combination with factors that affect population survival, the unusual species richness in haplochromine species flocks. I argue that sexual selection, if disruptive, can accelerate the pace of adaptive radiation because the resultant genetic population fragmentation allows a much increased rate of differential response to disruptive natural selection. Hence, the ecological pattern of diversity resembles that produced by disruptive natural selection, with the difference that disruptive sexual selection continues to cause (gross) speciation even after niche space is saturated. This may explain the unusually high numbers of very closely related and ecologically similar species in haplochromine species flocks. The role of disruptive sexual selection is twofold: it not only causes speciation, but also maintains reproductive isolation in sympatry between species that have evolved in sympatry or allopatry. Therefore, the maintenance of diversity in species flocks that originated through sexual selection depends on the persistence of the selection regime within the environmental signal space under which that diversity evolved.

The effect of dissolved magnesium on diffusion creep in calcite

We experimentally tested a series of synthetic calcite marbles with varying amounts of dissolved magnesium in a standard triaxial deformation machine at 300 MPa confining pressure, temperatures between 700 and 850°C, stresses between 2 and 100 MPa, and strain rates between 10−7 and 10−3 s−1. The samples were fabricated by hot isostatic pressing of a mixture of calcite and dolomite at 850°C and 300 MPa. The fabrication protocol resulted in a homogeneous, fine-grained high-magnesian calcite aggregate with minimal porosity and with magnesium contents between 0.07 and 0.17 mol% MgCO3. At stresses below 40 MPa the samples deformed with linear viscosity that depended inversely on grain size to the 3.26±0.51 power, suggesting that the mechanisms of deformation were some combination of grain boundary diffusion and grain boundary sliding. Because small grain sizes tended to occur in the high-magnesium calcite, the strength also appeared to vary inversely with magnesium content. However, the strength at constant grain size does not depend on the amount of dissolved magnesium, and thus, the impurity effect seems to be indirect. At stresses higher than 40 MPa, the aggregates become non-linearly viscous, a regime we interpret to be dislocation creep. The transition between the two regimes depends on grain size, as expected. The activation energy for diffusion creep is 200±30 kJ/mol and is quite similar to previous measurements in natural and synthetic marbles deformed at similar conditions with no added magnesium.